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- EMDB-9237: Rabbit 80S ribosome with P- and Z-site tRNAs (unrotated state) -

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Basic information

Entry
Database: EMDB / ID: 9237
TitleRabbit 80S ribosome with P- and Z-site tRNAs (unrotated state)
Map dataPostprocessed map
SampleRabbit 80S ribosome with a P- and Z-site tRNA (unrotated state)
  • (nucleic-acidNucleic acid) x 7
  • (60S ribosomal protein ...) x 43
  • (40S ribosomal protein ...) x 32
  • Receptor of activated protein C kinase 1
  • (ligand) x 2
Function / homologyRibosomal L28e/Mak16 / Ribosomal protein L32e superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L22/L17 superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L21 superfamily ...Ribosomal L28e/Mak16 / Ribosomal protein L32e superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L22/L17 superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein L21 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / 40S ribosomal protein S11, N-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L10e/L16 superfamily / RNA-binding S4 domain superfamily / Ubiquitin-like domain superfamily / Ribosomal protein L14 / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S4/S9 N-terminal domain / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ubiquitin-like protein FUBI / 40S Ribosomal protein S10 / Ribosomal protein L30/YlxQ / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / S27a-like superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L15 / 50S ribosomal protein L30e-like / Ubiquitin family / Ribosomal protein L5, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L18e/L15P / Ribosomal protein S19 conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein S7, conserved site / G-protein beta WD-40 repeat / Ribosomal protein L39e, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein S17, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S15P / Ribosomal protein S28e conserved site / Ribosomal protein L15e core domain superfamily / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / 30s ribosomal protein S13, C-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein S7 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Ribosomal protein L2, archaeal-type / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L16p/L10e / Ribosomal protein S17e signature. / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein S7 signature. / Ribosomal protein L39e signature. / Ribosomal protein L14 signature. / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal_S17 N-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S17 signature. / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S30 / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L6, N-terminal domain / Plectin/S10 domain / S25 ribosomal protein / Ribosomal protein S8 signature. / Ubiquitin domain signature. / Ribosomal protein L37e / Ribosomal protein S6e signature. / Ribosomal protein L6 signature 2. / Trp-Asp (WD) repeats signature. / Ribosomal protein S13 signature. / Ribosomal protein S4 signature. / Ribosomal protein L32e signature. / Ribosomal protein L29 signature. / Ribosomal protein S14 signature.
Function and homology information
SourceOryctolagus cuniculus (rabbit) / unidentified (others) / Rabbit (rabbit)
Methodsingle particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsBrown A / Baird MR / Yip MCJ / Murray J / Shao S
CitationJournal: Elife / Year: 2018
Title: Structures of translationally inactive mammalian ribosomes.
Authors: Alan Brown / Matthew R Baird / Matthew Cj Yip / Jason Murray / Sichen Shao
Abstract: The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. ...The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression.
Validation ReportPDB-ID: 6mtb

SummaryFull reportAbout validation report
DateDeposition: Oct 19, 2018 / Header (metadata) release: Nov 21, 2018 / Map release: Nov 21, 2018 / Last update: Nov 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6mtb
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9237.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.34 Å/pix.
= 536. Å
400 pix
1.34 Å/pix.
= 536. Å
400 pix
1.34 Å/pix.
= 536. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour Level:0.08 (by author), 0.08 (movie #1):
Minimum - Maximum-0.5671311 - 0.79736525
Average (Standard dev.)0.0015323462 (0.025479687)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.00.00.0
Limit399.0399.0399.0
Spacing400400400
CellA=B=C: 536.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z536.000536.000536.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.5670.7970.002

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Supplemental data

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Sample components

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Entire Rabbit 80S ribosome with a P- and Z-site tRNA (unrotated state)

EntireName: Rabbit 80S ribosome with a P- and Z-site tRNA (unrotated state)
Number of components: 86

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Component #1: protein, Rabbit 80S ribosome with a P- and Z-site tRNA (unrotated...

ProteinName: Rabbit 80S ribosome with a P- and Z-site tRNA (unrotated state)
Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #2: nucleic-acid, mRNA

Nucleic-acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CAAAGUU
MassTheoretical: 2.205379 kDa
SourceSpecies: unidentified (others)

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Component #3: nucleic-acid, P-site tRNA

Nucleic-acidName: P-site tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUCUCCGUAG UGUAGCGGUU AUCACGUUCG CCUAACACGC GAAAGGUCCU CGGUUCGAAA CCGGGCGGAA ACACCA
MassTheoretical: 24.436551 kDa
SourceSpecies: Rabbit (rabbit)

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Component #4: nucleic-acid, Z-site tRNA

Nucleic-acidName: Z-site tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCCCGGAUAG CUCAGCUGUA GAGCAUCAGA CUUUUAAUCU GAGGGUCCAG GGUUCAAGUC CCUGUUCGGG CGCCA
MassTheoretical: 24.102275 kDa
SourceSpecies: Rabbit (rabbit)

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Component #5: nucleic-acid, 28S rRNA

Nucleic-acidName: 28S rRNA28S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAA AAGAAACUAA CCAGGAUUCC CUCAGUAACG GCGAGUGAAC AGGGAAGAGC CCAGCGCCGA AUCCCCGCCC CGCGGCGGGG CGCGGGAAAU GUGGCGUACG GAAGACCCAC UCCCCGGCGC CGGGGGGCCC AAGUCCUUCU GAUCGAGGCC CAGCCCGUGG ACGGUGUGAG (B9B)CCGGUAGCG GCCCCCGGCG CGCCGGGCCC GGGUCUUCCC GGAGUCGGGU UGCUUGGGAA UGCAGCCCAA AGCGGGUGGU AAACUCCAUC UAAGGCUAAA UACCGGCACG AGACCGAUAG UCAACAAGUA CCGUAA(OMG)GGA AAGUUGAAAA GAACUUUGAA G(A2M)GAGAGUUC AAGAGGGCGU GAAACCGUUA AGAGGUAAAC GGGUGGGGUC CGCGCAGUCC GCCCGGAGGA UUCAACCCGG CGGCGCGGUC CGGCCGUGCC GGCGGGGCGG AUCUCCCGCU CCCGUCGGCG GGGGACCGCC CCCCGGCCGG CGACCGGCCG CCGCCGGGCG CAUUUCCACC GCGGCGGUGC GCCGCGACCG GCUCCGGGAC GGCU(2MG)GGAAG GCCCCGGCGG GGAAGGUGGC CCGGGGGCCC CGGGUGUUAC AGCCCCGCCC CGGCAGCAGC AGCUCGCCGA AUCCCGGGGC CGAGGGAGCG AGACCCGUGC CGCCGCGCUC UCCCCCCUGG GGGGGCCGGG CCACCCCUCC CACGGCGCGA CCGCUGGGGC GGACUGUCCA GUGCGCCCCG GGCGGGUCGC GCCGUCGGGC CCGGGGGGCC ACGCGUCCCC CGCGAGCGCA CGGGGUCGGC GGCGAUGUCG GCUACCCACC CGACCC(OMG)UCU UG(1MA)AAC(A2M)CGG ACCAAGGAGU CUAACACG(P4U)G CGCGAGUCGG GGGCUACGAA AGCCGCCGUG GCGCAAUGAA GGUGAAGGCC GGCGGCGCGC CGCCGGCCGA GGUGGGAUCC CGAGGCCUUC CAGUCCGCCG AGGG(B8Q)GCACC ACCGGCCCGU CUCGCCCGCC GCGCCGGGGA GGUGGAGCAC GAGCGCACGU GUUAG(2MG)ACCC (OMG)A(A2M)AGAUGGU GA(A2M)CUAUGCC UGGGCAGGGC GAAGCCAGAG GAAACUCUGG UG(B9B)AGGUCCG (PSU)AGCGGUCCU GACGUGCGAA UCG(7MG)UCGUCC GACCUGGGUA UAG(OMG)GGCGAA AGACUAAUCG AACCAUCUAG UAGCUGG(I4U)UC CCUCCAAAGU UUCCC(PSU)CAGG A(PSU)AGCUGGCG CUCUCCGCAG UUUUAUCCGG UAAAGCGAAU GAUUAGAGGU CUUGGGGCCG AAACGAUCUC AACCUAUUCU CAAACUUUAA AU(E7G)GGUAAGA AGCCCGGCUC GCUGGUGUGG AGCCGGGCGU GGAAUGCGAG UGCCUAGUGG GCCAC(B8H)UUUG G(UR3)AAGC(A2M)GAA CUGGCGCU(OMG)C GGGAUGAACC GAACGCCGGG UUAA(P7G)GCGCC CGAUGCCGAC GCUCAUCAGA CCCCAGAAAA GGUGUUGGUU GAUAUAGACA GCAGGAUGGU GGCCAUGGAA GUCGGAAUCC GCUAAGGAGU GUGUAACAAC UCACCUGCCG AAUCAACUAG CCCUGAAAAU GGAUG(OMG)CGCU GGAGCGUCGG GCCCAUACCC GGCCGUCGCU GGCAGUCGGC AGAGCGAGAA AGAGAGUGGC GCGGACGCUA CGCCGCGACG AGUAGGAGGG CCGCUGCG(E7G)U GAGCCUUGAA GCCUAGGGCG CGGGCCCGGG UGGAGCCGCC GCAGGUGCAG AUCUUGGUGG UAGU(A2M)(OMG)(OMC)AAA UAUUCAAACG A(B8W)AACUUUGA AGGCCGAAGU GG(A2M)GAAGGGU UCCAUGUGAA CAG(OMC)A(OMG)UUGA ACAUGGGUCA GUCGGUCCUG AGAGAUGGGC GAGCGCCGUU CCGAAGGGAC GGGCGAUGGC CUCCGUUGCC CUCAGCCGA(PSU) CGAAAGGGAG UCG(7MG)GUUCAG AUCCCCGAAU CCGGAGUGGC GGAGAUGGGC GCCGCGAGGC GUCCAGUGCG GUAACGCGAC CGAUCCCGGA GAAGCCGGCG GGAGCCCCGG GGAGAGUUCU CUUUUCUUUG UGAAGGGCAG GGCGCCCUGG AAUGGGUUCG CCCCGAGAGA GGGGCCCGUG CCUUGGAAAG CGUCGCGGUU CCGGCGGCGU CCGGUGAGCU CUCGCUGGCC CUUGAAAAUC CGGGG(B9B)AGAG GGUGUAAAUC UCGC(OMG)CCGGG CCGUACC(B9H)AU AUCCGCAGCA GGUCU(OMC)CAAG GUGAACAGCC UCUGGCAUGU UGGAACAAUG UAGGUAAGGG AAGUCGGCAA GC(OMC)GGAUCCG UAACUUCGGG AUAAGGAUUG GCUCUAAGGG CUGGCAGCCG ACUUAGAACU GGUGCGGACC AGGGGAAUCC GACUGUUUAA UUAAAACAAA GCAUCGCGAA GGCCCGCGGC GGGUGUUGAC GCGAUGUGAU UUCUGCC(OMC)AG UGCUCUGAAU G(PSU)CA(A2M)AGUG(A2M) AGAAA(PSU)UCAA UGAAGCGCGG GUAAACGGCG GGAGUAAC(B8H)A (PSU)GACUCUCUU AAGGUAGC(5MC)A A(A2M)UGCCUC(OMG)U CAUCUAAUUA GUGACGCGCA UGAAUGGAUG A(A2M)CGAGAUUC CCACUGUCCC UACCUACUAU CCAGCGAAAC CAC(A2M)G(OMC)CAAG GGAACG(P7G)GCU UGG(OMC)GGAAUC AGC(B8K)G(BGH)GAAA GAAGA(OMC)CCUG UUGAGCUUGA CUCUAGUCUG GCACGGUGAA GAGACAUGAG AAGUGUAGAA UAAGUGGGAG GCCGCCGGUG AAAUACCACU ACUCUGAUCG UUUUUUCACU GACCCGG(5MU)GA GGCGGGGGGG CGAGCCGGGC UCUCGCUUCU GGCGCCAA(B8W)C GCCCGGCCGG CCGGGCGCGA CCCGCUCCGG GGACAGUGCC AGGUGGG(B8W)AG UUUGAC(I4U)G(OMG)G GCGGUACACC UGUCAAACGG UA(6MZ)CGCAGGU GUCCUAAGGC GAGCUCAGGG AGGACAGAAA CCUCCCGUGG AGCAGAAGGG CAAAAGCUCG CUUGA(PSU)CU(B8H)G AUUUUCAG(OMU)A CGAAUACAGA CCGUGAAAGC GGGGCCU(5MC)AC GAUCCUUCUG ACCUUUU(E6G)GG UUUUAAGCAG GA(OMG)(MHG)UGUCAG AAAAGUUACC ACAGGGAUAA CUGGC(PSU)UGUG GCGGCCA(1MA)GC GUUCAUAGCG ACGUCGCUUU UUGA(PSU)CCUU(5MC) GA(PSU)GUCGGCU CUUCCUAUCA UUGU(B8W)AAGCA GAAUU(B8T)ACCA AGCGUU(OMG)GAU UG(PSU)UCACCCA CUAAUAGGGA ACGUG(A2M)GCUG G(B8W)(UR3)(PSU)UAGA(OMC)C GUCGUGAGAC AG(7MG)UUAGUUU UACCCU(M7A)CUG AUG(A2M)UGUGUU GUUGCCAUGG UAAUCCUGC(UR3) CAGUACGAGA GGAACCGCAG GU(OMU)CA(OMG)ACAU (PSU)UGGUGUA(PSU)(OMG) UGCUUGGCUG AGGAGCCAAU GGGGCGAAGC UAC(B8T)AUCUGU GGGAUUAUGA CU(B8K)AACGCCU CUAAGUCAGA AUCCCGCCCA GGCGGAACGA UAGCGCCGGA GCCUCGGUUG GCCUCGGAUA GCCGGUCCCC CGCCGGGGUC CGGU(OMG)C(2MG)GAG AGCCCUUCGU CCCGGGAAAC GGGGCGGCCG GAAAGGGGGC CGCCCUCUCG CCCGUCACGC ACCGCACGUU CGUGGGGAAC CUGGCGCUAA ACCAUUCGUA GACGACCUGC UUCUGGGUCG GGGUUUCGUA CGUAGCAGAG CAGCUGCUGC GAUCUAUUGA AAGUCAGCCC UCGACACAAG GGUUUGU
MassTheoretical: 1.167366125 MDa
SourceSpecies: Rabbit (rabbit)

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Component #6: nucleic-acid, 5S rRNA

Nucleic-acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUCUACGGCC AUACCACCCU GAACGCGCCC GAUCUCGUCU GAUCUCGGAA GCUAAGCAGG GUCGGGCCUG GUUAGUACUU GGAUGGGAGA CCGCCUGGGA AUACCGGGUG CUGUAGGCUU
MassTheoretical: 38.691914 kDa
SourceSpecies: Rabbit (rabbit)

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Component #7: nucleic-acid, 5.8S rRNA

Nucleic-acidName: 5.8S rRNA5.8S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGACUCUUAG CGG(OMU)GGAUCA CUCGGCUCGU GCGUCGAUGA AGAACGCAGC UAGCUGCGAG AAUUAAUGUG AAUUGCAGGU UGAUCAUCGA CACUUCGAAC GCACUUGCGG CCCCGGGUUC CUCCCGGGGC UACGCCUGUC UGAGCGUCGC U
MassTheoretical: 48.559699 kDa
SourceSpecies: Rabbit (rabbit)

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Component #8: protein, 60S ribosomal protein L8

ProteinName: 60S ribosomal protein L8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.998613 kDa
SourceSpecies: Rabbit (rabbit)

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Component #9: protein, 60S ribosomal protein L3

ProteinName: 60S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.119812 kDa
SourceSpecies: Rabbit (rabbit)

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Component #10: protein, 60S ribosomal protein L4

ProteinName: 60S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.114434 kDa
SourceSpecies: Rabbit (rabbit)

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Component #11: protein, 60S ribosomal protein L5

ProteinName: 60S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.077391 kDa
SourceSpecies: Rabbit (rabbit)

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Component #12: protein, 60S ribosomal protein L6

ProteinName: 60S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.028336 kDa
SourceSpecies: Rabbit (rabbit)

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Component #13: protein, 60S ribosomal protein L7

ProteinName: 60S ribosomal protein L7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.201836 kDa
SourceSpecies: Rabbit (rabbit)

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Component #14: protein, 60S ribosomal protein L7a

ProteinName: 60S ribosomal protein L7a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.221516 kDa
SourceSpecies: Rabbit (rabbit)

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Component #15: protein, 60S ribosomal protein L9

ProteinName: 60S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.627215 kDa
SourceSpecies: Rabbit (rabbit)

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Component #16: protein, 60S ribosomal protein L10

ProteinName: 60S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.643057 kDa
SourceSpecies: Rabbit (rabbit)

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Component #17: protein, 60S ribosomal protein L11

ProteinName: 60S ribosomal protein L11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.288465 kDa
SourceSpecies: Rabbit (rabbit)

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Component #18: protein, 60S ribosomal protein L13

ProteinName: 60S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.200525 kDa
SourceSpecies: Rabbit (rabbit)

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Component #19: protein, 60S ribosomal protein L14

ProteinName: 60S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.217355 kDa
SourceSpecies: Rabbit (rabbit)

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Component #20: protein, 60S ribosomal protein L15

ProteinName: 60S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.076088 kDa
SourceSpecies: Rabbit (rabbit)

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Component #21: protein, 60S ribosomal protein L13a

ProteinName: 60S ribosomal protein L13a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.144859 kDa
SourceSpecies: Rabbit (rabbit)

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Component #22: protein, 60S ribosomal protein L17

ProteinName: 60S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.758678 kDa
SourceSpecies: Rabbit (rabbit)

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Component #23: protein, 60S ribosomal protein L18

ProteinName: 60S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.568492 kDa
SourceSpecies: Rabbit (rabbit)

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Component #24: protein, 60S ribosomal protein L19

ProteinName: 60S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.613033 kDa
SourceSpecies: Rabbit (rabbit)

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Component #25: protein, 60S ribosomal protein L18a

ProteinName: 60S ribosomal protein L18a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.827561 kDa
SourceSpecies: Rabbit (rabbit)

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Component #26: protein, 60S ribosomal protein L21

ProteinName: 60S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.478791 kDa
SourceSpecies: Rabbit (rabbit)

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Component #27: protein, 60S ribosomal protein L22

ProteinName: 60S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.495275 kDa
SourceSpecies: Rabbit (rabbit)

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Component #28: protein, 60S ribosomal protein L23

ProteinName: 60S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.972425 kDa
SourceSpecies: Rabbit (rabbit)

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Component #29: protein, 60S ribosomal protein L24

ProteinName: 60S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.825111 kDa
SourceSpecies: Rabbit (rabbit)

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Component #30: protein, 60S ribosomal protein L23a

ProteinName: 60S ribosomal protein L23a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.727181 kDa
SourceSpecies: Rabbit (rabbit)

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Component #31: protein, 60S ribosomal protein L26

ProteinName: 60S ribosomal protein L26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.891787 kDa
SourceSpecies: Rabbit (rabbit)

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Component #32: protein, 60S ribosomal protein L27

ProteinName: 60S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.704635 kDa
SourceSpecies: Rabbit (rabbit)

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Component #33: protein, 60S ribosomal protein L27a

ProteinName: 60S ribosomal protein L27a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.489363 kDa
SourceSpecies: Rabbit (rabbit)

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Component #34: protein, 60S ribosomal protein L29

ProteinName: 60S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.708707 kDa
SourceSpecies: Rabbit (rabbit)

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Component #35: protein, 60S ribosomal protein L30

ProteinName: 60S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.914756 kDa
SourceSpecies: Rabbit (rabbit)

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Component #36: protein, 60S ribosomal protein L31

ProteinName: 60S ribosomal protein L31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.635694 kDa
SourceSpecies: Rabbit (rabbit)

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Component #37: protein, 60S ribosomal protein L32

ProteinName: 60S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.022021 kDa
SourceSpecies: Rabbit (rabbit)

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Component #38: protein, 60S ribosomal protein L35a

ProteinName: 60S ribosomal protein L35a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.449612 kDa
SourceSpecies: Rabbit (rabbit)

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Component #39: protein, 60S ribosomal protein L34

ProteinName: 60S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.994621 kDa
SourceSpecies: Rabbit (rabbit)

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Component #40: protein, 60S ribosomal protein L35

ProteinName: 60S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.435403 kDa
SourceSpecies: Rabbit (rabbit)

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Component #41: protein, 60S ribosomal protein L36

ProteinName: 60S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.888371 kDa
SourceSpecies: Rabbit (rabbit)

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Component #42: protein, 60S ribosomal protein L37

ProteinName: 60S ribosomal protein L37 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.090891 kDa
SourceSpecies: Rabbit (rabbit)

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Component #43: protein, 60S ribosomal protein L38

ProteinName: 60S ribosomal protein L38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.107752 kDa
SourceSpecies: Rabbit (rabbit)

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Component #44: protein, 60S ribosomal protein L39

ProteinName: 60S ribosomal protein L39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.324579 kDa
SourceSpecies: Rabbit (rabbit)

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Component #45: protein, 60S ribosomal protein L40

ProteinName: 60S ribosomal protein L40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.212593 kDa
SourceSpecies: Rabbit (rabbit)

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Component #46: protein, 60S ribosomal protein L41

ProteinName: 60S ribosomal protein L41 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.473451 kDa
SourceSpecies: Rabbit (rabbit)

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Component #47: protein, 60S ribosomal protein L36a

ProteinName: 60S ribosomal protein L36a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.070474 kDa
SourceSpecies: Rabbit (rabbit)

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Component #48: protein, 60S ribosomal protein L37a

ProteinName: 60S ribosomal protein L37a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.168153 kDa
SourceSpecies: Rabbit (rabbit)

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Component #49: protein, 60S ribosomal protein L28

ProteinName: 60S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.220686 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #50: protein, 60S ribosomal protein L10a

ProteinName: 60S ribosomal protein L10a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.599887 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #51: nucleic-acid, 18S rRNA

Nucleic-acidName: 18S rRNA18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UACCUGGUUG AUCCUGCCAG UAGCAU(A2M)UGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGU(OMU)CC(PSU)U (OMU)GGUCGCUCG UACUUGGAUA ACUGUGGUA(A2M) UUCUAG(A2M)GCU AAUA(OMC)AUGCC GACGGGCGCU GACCCCCUUC GCGGGGGGGA UGCGUGCAUU UAUCAGUGGU GACUCUAGAU AACCUCGGGC CGAUCGCACG CCCGGCGGCG ACGACCCAUU CGAACGUCUG CCCUAUCAAC UUUCGAUGGU AGUCGCCGUG CCUACCAUGG UGACCACGGG UGACGGGGAA UCAGGGUUCG AUUCCGGAGA GGGAGCCUGA GAAACGGCUA CCACAUCCAA GGAAGGCAGC AGGCGCGC(A2M)A AUUACCCACU CCCGACCCGG GGA(OMG)GUAGUG A(OMC)GAAAAAUA ACAAUACAGG ACUCUUUCGA GGCCCUGUAA UUGGAAUGAG UC(E3C)ACUUUAA AUCCUUUAAC GAGGAUCCAU UGGAGGGCAA GUCUGG(PSU)GCC AGCAGCCGCG GUAAUUCCAG CUCCAAUA(OMG)C GUAUAUUAAA GUUGCUGCAG UU(A2M)AAAAGCU CGUAGUU(OMG)GA UCUUGGGAGC GGCCGUCCCC UGCUCGGCGC CGGCCCGAAG CGUUUACUUU GAAAAAA(5MU)UA GAGUG(PSU)(PSU)CAA AGCAGGCCGC CUGGAUACCG CAGCUAGGAA UAAUGGAAUA GGACCGCGGU UCUAUUUUGU UGGUUUUCGG AACUGAGGCC AUGAUUAAGA GGGACGGCCG GGGGCAUUCG UAUUGCGCCG CUAGAGGUGA AAUUCUUGGA CCGGCGCAAG ACGGACCAGA GCGAAAGCAU UUGCCAAGAA UGUUUUCAUU AAUCAAGA(A2M)C GAAAGUCGGA GGUUCGAAGA CGAUCAGAUA CCGUCGUAGU UCCGACCA(PSU)A AACGAUGCCG ACUGGCGAUG CGGCGGCGUU AUUCCCAUGA CCCGCCGGGC AGCUUCCGGG AAACCAAAGU CUUUGGGUUC CGGGGGGAGU AUGGUUGCAA AGCUGAAACU UAAAGGAAUU GACGGAAGGG CACCAC(B8Q)AGG AGUGGAGCCU GCGGCUUAAU (PSU)UGAC(B8N)CAAC ACGGGAAACC UCACCCGGCC CGGACACGGA CAGGAUUGAC AGAUUGAUAG CUCUUUCUCG AUUCCGUGGG UGGUGGUGCA UGGC(4AC)GUUCU UAGUUGGUGG AGCGAUUUGU CUGGUUAAUU C(5MC)GAUAACGA ACGAGACUCU GGCAUGCUAA CUAGUUACGC GACCCCGGUC GGCGUAACUU CUUAGAGGGA CAAGUGGCGU UCAGCCACCC GAGAUUGAGC AAUAACAGGU CUGUGAUGCC CUUAGAUGUC CGGGGCUGCA CGCGCGCUAC ACUGACUGGC UCAGCGUGUG CCUACCCUAC GCCGGCAGGC GCGGGUAACC CGUUGAACCC CAUUCGUGAU GGGGAUCGGG GAUUGCAAUU AUUCCCCAUG AACGAGGAAU UCCCAGUAAG UGCGGGUCAU AAGCUUGCGU UGAUU(A2M)AGUC CCUGCCCUUU GUACACACCG (OMC)CCGUCG(OMC)UA CUACCGAUUG GAUGGUUUAG UGAGGCCCUC GGAUCGGCCC CGCCGGGGUG CCCUGGCGGA GCGCUGAGAA GACGGUCGAA CUUG(M7A)CUAUC UAGAGGAAGU AAAAGUCG(UR3)A (6MZ)CAAGGUUUC (4AC)GUAGGUG(MA6)(MA6) CCUGCGGAAG GAUCAUUA
MassTheoretical: 548.638062 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #52: protein, 40S ribosomal protein SA

ProteinName: 40S ribosomal protein SA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.361861 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #53: protein, 40S ribosomal protein S3a

ProteinName: 40S ribosomal protein S3a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.759145 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #54: protein, 40S ribosomal protein S2

ProteinName: 40S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.441846 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #55: protein, 40S ribosomal protein S3

ProteinName: 40S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.215586 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #56: protein, 40S ribosomal protein S4, X isoform

ProteinName: 40S ribosomal protein S4, X isoformRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.523674 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #57: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.913453 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #58: protein, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.471535 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #59: protein, 40S ribosomal protein S7

ProteinName: 40S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.168914 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #60: protein, 40S ribosomal protein S8

ProteinName: 40S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.003012 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #61: protein, 40S ribosomal protein S9

ProteinName: 40S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.649633 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #62: protein, 40S ribosomal protein S10

ProteinName: 40S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.529682 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #63: protein, 40S ribosomal protein S11

ProteinName: 40S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.468826 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #64: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.048244 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #65: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.057113 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #66: protein, 40S ribosomal protein S14

ProteinName: 40S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.544659 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #67: protein, 40S ribosomal protein S15

ProteinName: 40S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.246854 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #68: protein, 40S ribosomal protein S16

ProteinName: 40S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.032804 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #69: protein, 40S ribosomal protein S17

ProteinName: 40S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.250714 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #70: protein, 40S ribosomal protein S18

ProteinName: 40S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.898648 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #71: protein, 40S ribosomal protein S19

ProteinName: 40S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.611003 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #72: protein, 40S ribosomal protein S20

ProteinName: 40S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.395489 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #73: protein, 40S ribosomal protein S21

ProteinName: 40S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.124389 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #74: protein, 40S ribosomal protein S15a

ProteinName: 40S ribosomal protein S15a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.734357 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #75: protein, 40S ribosomal protein S23

ProteinName: 40S ribosomal protein S23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.626392 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #76: protein, 40S ribosomal protein S24

ProteinName: 40S ribosomal protein S24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.432125 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #77: protein, 40S ribosomal protein S25

ProteinName: 40S ribosomal protein S25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.526119 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #78: protein, 40S ribosomal protein S26

ProteinName: 40S ribosomal protein S26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.645794 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #79: protein, 40S ribosomal protein S27

ProteinName: 40S ribosomal protein S27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.34899 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #80: protein, 40S ribosomal protein S28

ProteinName: 40S ribosomal protein S28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.007069 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #81: protein, 40S ribosomal protein S29

ProteinName: 40S ribosomal protein S29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.559625 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #82: protein, 40S ribosomal protein S30

ProteinName: 40S ribosomal protein S30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.317539 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #83: protein, 40S ribosomal protein S27a

ProteinName: 40S ribosomal protein S27aRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.98644 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #84: protein, Receptor of activated protein C kinase 1

ProteinName: Receptor of activated protein C kinase 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.669113 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #85: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 297 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #86: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
Support filmunspecified
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 62560
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 5LZV
Output model

+
About Yorodumi

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Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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